Where does a .blend file store its user preferences?
C:\Users\ [UserName] \AppData\Roaming\Blender Foundation\Blender there are folders for each version (2.72, 2.73) where data is stored.

Appdata folder is hidden by default, you can change windows settings or enter the path it manually in explorer

It's not specific to your blend file but blender's preferences. A blend file stores it's data inside the blend files. But you can prevent some prefs to be loaded with unchecking "load UI" when opening a file.



Or you can change blender preferences unchecking "Load UI" and "aurorun python scripts".



Once the file is opened, you can check what's needed and save a clean version of it.